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https://github.com/MillironX/nf-core_modules.git
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Add beautiful md5sums
This commit is contained in:
FriederikeHanssen
parent
5e365d5eff
commit
13733b2581
3 changed files with 58 additions and 10 deletions
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@ -50,7 +50,8 @@ process SEQKIT_SPLIT2 {
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 $reads
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-1 ${reads} \
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--out-dir ${prefix}.split
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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"""
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@ -61,7 +62,9 @@ process SEQKIT_SPLIT2 {
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$options.args \
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--threads $task.cpus \
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-1 ${reads[0]} \
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-2 ${reads[1]}
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-2 ${reads[1]} \
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--out-dir ${prefix}.split
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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@ -3,8 +3,8 @@
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nextflow.enable.dsl = 2
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 5000' ] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2'] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 200' ] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 3'] )
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workflow test_seqkit_split2_single_end_length {
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def input = []
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@ -6,7 +6,11 @@
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- seqkit_split2_single_end
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- length
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files:
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- path: output/seqkit/
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- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
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md5sum: fb45cfec0d0d37f85abe81a0d299137e
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- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
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md5sum: 0dfb5284ee0bb7e1b77b57dc1bd16311
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- name: seqkit split2 single-end size
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
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@ -16,7 +20,12 @@
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- seqkit_split2_single_end
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- size
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files:
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- path: output/seqkit/
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- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
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md5sum: e76ac276819eb862c0a931755a220b50
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- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
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md5sum: 79eb15ff1aac645308fab188915f9edf
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- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
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md5sum: f01fa62d34012a2e9cc48972dfe8c14c
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- name: seqkit split2 single-end part
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
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@ -26,7 +35,12 @@
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- seqkit_split2_single_end
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- part
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files:
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- path: output/seqkit/
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- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
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md5sum: c394bc973e1f0f9bda835e4a7610d2e1
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- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
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md5sum: 152e4470b8caeed1fc1c0326f34aa4e6
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- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
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md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d
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- name: seqkit split2 paired-end length
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
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@ -36,7 +50,14 @@
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- seqkit_split2_paired_end
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- length
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files:
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- path: output/seqkit/
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- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
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md5sum: fb45cfec0d0d37f85abe81a0d299137e
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- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
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md5sum: 0dfb5284ee0bb7e1b77b57dc1bd16311
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- path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz
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md5sum: 4e9704a4a0f4bcab4900b6fcd9323d8a
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- path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz
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md5sum: da93241d0cfa84d4b806e1e102c16977
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- name: seqkit split2 paired-end size
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
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@ -46,7 +67,18 @@
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- seqkit_split2_paired_end
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- size
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files:
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- path: output/seqkit/
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- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
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md5sum: e76ac276819eb862c0a931755a220b50
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- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
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md5sum: 79eb15ff1aac645308fab188915f9edf
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- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
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md5sum: f01fa62d34012a2e9cc48972dfe8c14c
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- path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz
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md5sum: 357bfa5b981f34d87f682aebcf5e46fe
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- path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz
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md5sum: f48f3389d2870f4934139a901e5c4bb2
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- path: output/seqkit/test.split/SRR396636_R2.part_003.fastq.gz
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md5sum: d161aa05bac2f7d1823da0479949512b
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- name: seqkit split2 paired-end part
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
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@ -54,4 +86,17 @@
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- seqkit
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- seqkit_split2
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- seqkit_split2_paired_end
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- part
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- part
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files:
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- path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz
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md5sum: c394bc973e1f0f9bda835e4a7610d2e1
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- path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz
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md5sum: 152e4470b8caeed1fc1c0326f34aa4e6
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- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
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md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d
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- path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz
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md5sum: 228aff8f1e56050967476fcad164a4fc
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- path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz
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md5sum: 41047f3df10126c0df7f8e9bfd752b83
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- path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz
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md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d
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